rTASSEL: an R interface to TASSEL for association mapping of complex traits

The need for efficient tools and applications for analyzing genomic diversity is essential for any genetics research program. One such tool, TASSEL (Trait Analysis by aSSociation, Evolution and Linkage), provides many core methods for genomic analyses. Despite its efficiency, TASSEL has limited mean...

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Bibliographic Details
Published inbioRxiv
Main Authors Monier, Brandon, Casstevens, Terry M, Bradbury, Peter J, Buckler, Edward S
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 31.03.2021
Subjects
Gene mapping
Genomic analysis
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Summary:The need for efficient tools and applications for analyzing genomic diversity is essential for any genetics research program. One such tool, TASSEL (Trait Analysis by aSSociation, Evolution and Linkage), provides many core methods for genomic analyses. Despite its efficiency, TASSEL has limited means to use scripting languages for reproducible research and interacting with other analytical tools. Here we present an R package rTASSEL, a front-end to connect to a variety of highly used TASSEL methods and analytical tools. The goal of this package is to create a unified scripting workflow that exploits the analytical prowess of TASSEL in conjunction with R's popular data handling and parsing capabilities without ever having the user to switch between these two environments. By implementing this workflow, we can achieve performances ranging from approximately 3 to 12 times faster than other widely used R packages for various functionalities. Competing Interest Statement The authors have declared no competing interest. Footnotes * Reduced wording and added performance metrics of various functionalities in supplemental information.
DOI:10.1101/2020.07.21.209114